User: harmadikemil

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Posts by harmadikemil

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Comment: C: Extract information from txt
... Thank you, it worked perfectly! I would have an another question. Can I make a list of sequences with grep? For example: Pasteurella multocida query: NB501791:62:HLKV3AFXY:3:11601:15774:10353 1:N:0:AAGCAGA query: NB501791:62:HLKV3AFXY:3:11601:15774:10353 1:N:0:AAGCAGA query: NB ...
written 5 weeks ago by harmadikemil0
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Extract information from txt
... Dear All! I have a txt with this kind of information: query: NB501791:62:HLKV3AFXY:4:21507:10794:16613 1:N:0:AAGCAGA match:gi|1548994288|gb|CP034492.1| Eukaryotic synthetic construct chromosome 14 >gi|1549096114|gb|CP034517 match:gi|1351431640|ref|XM_024231364.1| PREDICTED: Pongo ab ...
archeogenetics python sequence blast written 5 weeks ago by harmadikemil0
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Comment: C: How i can extract the first hit's title from blast XML-s
... Thank you for the fast aswer! I wrote a short code, but my problem, that i don't know how to reach the hit_num part in the xml. My code is: x=1 for record in NCBIXML.parse(open("full_result.xml")): if record.alignments: print("\n") print("query: %s" %record.q ...
written 5 weeks ago by harmadikemil0
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How i can extract the first hit's title from blast XML-s
... Dear All! i'm new to bioinformatics, and i'm working on an archeogenetics project. My first task, that in a genome part i should search the contaminating, non-human segments. It's a ~500 shotgun sequence. I would have two questions: -How could i print out just the first hits from the XML. -How c ...
python biopython written 6 weeks ago by harmadikemil0

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